


Crypsis

by zoemathemata



Category: Stargate Atlantis
Genre: Alpha John Sheppard, Alpha/Beta/Omega Dynamics, Lying About Identity, M/M, Omega Rodney McKay, Omega-ist attitudes, Secret Relationship, Stereotypes, somewhat canon compliant
Language: English
Status: Completed
Published: 2016-02-03
Updated: 2016-02-03
Packaged: 2018-05-17 23:39:04
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 9,782
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/5889556
Author URL: https://archiveofourown.org/users/zoemathemata/pseuds/zoemathemata
Summary: <blockquote class="userstuff">
              <p>Rodney McKay is the pissiest Alpha John Sheppard has ever met. And that’s saying something.</p>
            </blockquote>





	Crypsis

**Author's Note:**

  * For [melagan](https://archiveofourown.org/users/melagan/gifts).



> I changed the canonical order of the episodes. In this ‘verse, The Defiant One happens BEFORE the Storm and the Eye. Because of *reasons*. 
> 
> Also, this is what happens when melagan says she doesn’t have all the days of Romancing McShep filled and I say, ‘Oh, I can write a little something!’ Also, I would like to 'gift' this to her - even though there's no porn. SORRY. 
> 
> I didn’t have time to plot, get a beta or work out all the actual background of this - but hey, here's approx 10000 of McShep, lol. I hope you enjoy!

Rodney McKay is the pissiest Alpha John Sheppard has ever met. 

And that’s saying something. 

John grew up around his father and his father’s business associates. Alphas who had silver spoons in their mouths and up their asses. Alphas that got what they wanted, when they wanted, how they wanted and never even had a thought there was any other way to live. 

Then, John joined the Air Force and if he thought he knew pissy Alphas before that…. Well, the Air Force disabused him of that notion quickly. Pilots were always known to be particular about things. Their belongings, their flight plans, their lives. Military Alpha pilots were like operatic divas. If it didn’t go their way, it didn’t go any way at all. 

John was used to dealing with Alphas that liked to throw their weight around. He’d grown up with bossy, angry, entitled Alphas, so it hadn’t been a shock to become an officer and be surrounded by it every day. However, for the other officers, this was probably the first time in their life they weren’t part of the minority. Since only about thirty percent of the population were Alphas, they were used to being a little bit special. Coupled with the natural inclination of betas to follow an Alpha’s lead and Alphas were more than a little entitled. 

All that considered, it’s pretty impressive that McKay is the pissiest Alpha John has ever met. 

“Major, think about where we are in the solar system…”

***

John knows he’s considered oddly laid back for an Alpha. Maybe it’s because he got tired of the posturing from his father and his father’s business associates at a young age, maybe it’s because he spent too much time with his beta brother Dave, or maybe it’s because he always kind of took after his Omega mother. Quiet and soft-spoken, she had a fragility about her that most Omegas had - always looking like she was about to bolt out of the room at a loud sound or quick movement. John always preferred her company to that of his father - something he doesn’t think his father has ever forgiven him for. Not that John’s ever asked. He figures his father can add it to the long list of other things he thinks John should apologize and beg forgiveness for. For not being a typical Alpha, for not being loud, boisterous and overtly masculine, for not being broad of shoulder, narrow of hip and ready to defend anything he wants with brute force. For not taking his place in his father’s company, for joining the military, _the military for god’s sake_ , and then not even taking the position his father tried to wrangle for him as a military advisor but having the gall, the nerve, the audacity to want to fly planes. 

John really doesn’t give two shits what most people think an Alpha should do or be. What _he_ should do or be. 

McKay is a bulldozer of an Alpha, but he’s got the brains to back it up. He’s loud, he barks orders, he’s not afraid to give his opinion, then tell you what your opinion should be and then mock you for your actual opinion once you express it. 

Although to be fair, McKay’s right a lot of the time. John can see why he made it on the expedition. The other scientists are all brilliant, and the officers and enlisted men are no slouches in the brain department either, but McKay’s able to make connections at lightning speed and will make decisions just as fast when required. 

But… there’s still something just a little off about him. John can’t put his finger on it, but it’s there, niggling at his brain. It’s not like he has time to think about it - Sumner dying and John being in charge, meeting the Athosians, setting up a gate team and starting to explore Pegasus - these things don’t lend themselves to long, introspective moments where John can pause and let his brain turn something over. He’s smart, but clearly he’s no McKay. There’s something that pokes at John, but since it’s not life threatening, he doesn’t have time to worry about it. 

***

Sometimes Omegas make John uncomfortable. When they’re scared or worried, they have this way of looking at you - big eyes, anxious expression, distraught face. Their accompanying pheromones and hormones make it nearly impossible for John to ignore his own biological response and he ends up gracelessly trying to comfort and console an Omega. It’s always awkward. While he knows he’s fulfilling a biological function (Omegas gets scared, releases pheromones; Alpha responds, releases counterpoint pheromones; Omega calms down, releasing new pheromones; Alpha responds, own pheromones calming; both parties getting a surge of oxytocin and dopamine; everyone wins), it still makes him uncomfortable, like a suit that doesn’t fit. There was one time he ran into a crying Radek in the hallway and asked if he was okay. Radek clutched at him wildly, fisting his hands in John’s uniform and holding on for dear life while he sobbed into John’s shirt. John wildly eyeballed any Alpha, Beta or Omega who happened to pass by, silently ordering them to come relieve him from his Omega calming duty. God bless Lorne. Lorne happened by and took pity on him, somehow managing to coax Radek away and leading him back toward the science lab. John later found out Lorne managed to round up two other Omegas and a couple of ‘softer’ betas, sending them all to the mess hall for some snacks and bonding time. 

God bless him. John’s gonna promote that guy. 

Omegas only make up seven percent of the population on Earth, but John’s seen the numbers for the distribution in Atlantis and is surprised to find out he’s got a population of twelve percent of Omegas on his hands. But, there’s also a higher number of Alphas on Atlantis versus Earth due to the proportion of military officers. The military is a good fit for Alphas - plays to their strengths - leadership, brute force (at times), decision making, protecting those that cannot protect themselves. John wondered how the social dynamics would play out with the shifted percentages, but so far there haven’t been any issues. The Omegas are happy to have a high number of Alphas around to boost them if necessary and the Alphas walk around with a perpetual swagger - feeling rather needed and in demand given the high quantities of Omegas. The Betas don’t seem to notice or care that there’s a slightly different dynamic on Atlantis than at home. 

Teyla finds it all endlessly interesting. The Athosians aren’t biologically structured like the earthlings are. There are no Alphas, Betas or Omegas. There are other planets in Pegasus with the same dynamics, but Teyla doesn’t know as much about them. Elizabeth is already writing a dissertation on the differences between Athosian social mores and Earth’s with Teyla’s assistance - trying to determine what’s due to the influence of the Wraith, and what’s due to the lack of an A/B/O structure. Elizabeth wonders if the A/B/O dynamic is due to some genetic mutation the Ancients introduced as part of their bid for Ascension. Or maybe to help increase the fertility of the Pegasus galaxy to counteract the Wraith feeding. God knows the Ancients liked to fuck around with things. 

Beckett is a textbook Omega. Caring, reserved, doesn’t want to argue or fight, a little timid. Of course, like most Omegas, if you get in the way of him caring for someone, he’ll push you out of the way and give you a tongue lashing that will make your ears burn, but for the most part, his Omega nature coupled with his obvious skill and knowledge in medicine, make him the perfect doctor. Omegas like him because he’s non-threatening, Betas like him because he’s caring and knowledgeable and Alphas like him because his presence is soothing and soft. 

Which is why it’s a surprise when John enters the medlab one day to see McKay and Beckett arguing in Beckett’s office. He can’t hear anything (damn Atlantis and her sound proof walls), but the clear glass of Beckett’s office gives a great view and there’s no mistaking what’s happening. There’s a lot of finger pointing and waving from McKay and then some hand-wringing and earnest eyes from Beckett. McKay’s mouth does that sideways down-turn thing. John probably shouldn’t know McKay’s mouth that well, but he finds himself staring at it from time to time. It, and the rest of McKay’s face, is just so expressive. Everything about McKay seems…. _more_. He’s more loud, more abrasive, more intelligent and, if John’s being honest, McKay looks just as good walking away from someone as he does coming toward them. He’s seen McKay staring at him at times too, his blue eyes moving away quickly and sharply when he thinks he’s been caught. Maybe McKay’s one of those hetero-dynamic supporters that thinks an Alpha-Alpha relationship is a bad idea, or wrong. It would be disappointing to John if that’s the case. He didn’t figure McKay for one of those puritan types. Although… there were a couple of chummy Omegas in the science contingent and John knows McKay has seen them and he hasn't said anything about it. 

McKay stands in Beckett’s office, hands resting on Beckett’s desk as he leans over it, saying… something. Something heated. Beckett stands too, his own fingers starting to poke at the table and then at McKay, his kind face going a little red. Huh. Good for him. An Omega standing up to an Alpha is not unheard of, but it is rare. Beckett seems to be holding his own against McKay. John doesn’t like any Omega being bullied and he would hate to think McKay is doing that to Beckett. But if he’s trying, Beckett doesn’t seem to be having any of it. McKay crosses his arms and straightens his spine - a classic Alpha move to assert dominance. And Beckett… was that a snort? Wow, the doc is really giving as good as he gets. Though it’s probably rude of John, he knocks on the office glass to interrupt. Both Beckett and McKay turn to the glass window, equal expressions of surprise and displeasure on their faces. John gives a cheery, smart-alecky wave, knowing a smirk is curling his own lips. McKay turns and says one final thing to Beckett and Beckett pauses and then nods. He doesn’t look happy about it, but he seems to agree with whatever McKay says. 

The door opens and John is hit with the scent of ‘distressed Omega.’

“Problem, McKay?” he asks, eyes flicking to Beckett and then back to McKay. 

McKay’s chin juts out slightly, his cool blue eyes raking up and down John before meeting his gaze head on. “Nothing to worry about, Major.”

John looks back to Beckett. Again, there’s something tickling his grey matter but he’s not sure what it is. Beckett, in typical Omega fashion, looks away when John stares at him for too long, busying himself with clearing some papers on his desk. John turns to McKay who’s already stepped past him and is on his way out of medlab. 

“See you at the gate tomorrow,” John calls. McKay raises his hand in a sort of flapping wave, indicating he heard John, but he doesn’t turn around as he exits the lab. 

Leaning against the door jamb, John crosses his arms and looks at Beckett. 

“Can I help you, Major?” Beckett asks, all wide eyes and earnest Omega heart. 

“Is McKay bothering you?” John asks, even as he hates to. The thought of McKay hassling Beckett irks and disappoints him. McKay’s pissy but John didn’t think he was that kind of Alpha - the kind that harasses Omegas. 

“Rodney?” Becket asks, his eyes going even wider, his tone incredulous. The way he clearly thinks it’s ridiculous makes John relax. 

“It seems I interrupted something,” John says, head tilting toward the door McKay just exited.

Beckett’s shoulders slump and he struggles for his words. “We’ve known each other a long time.”

John nods, casually stepping into Beckett’s office. “It’s rare for an Alpha and Omega to be friends.”

Beckett’s eyes immediately go suspicious. “It shouldn’t be.”

“No, you’re right, it shouldn’t be, but it is.” John’s stomach clenches for a moment. Are McKay and Beckett together? Is that why they’re arguing? They do tend to interact like an old married couple - snarking and arguing with each other. John inhales and then regrets it - the smell of ‘upset Omega’ floods his nostrils. Goddamn, he’s going to have to hug Beckett and unless Lorne shows up magically again, there won’t be an impromptu rescue. It smells like anxiety, fear and distress in Beckett’s office and John’s Alpha instincts are going haywire. Almost unwilling, he takes a step closer to Beckett. Beckett strangely doesn't seem to notice and sits back down in his seat with a loud ‘thump.’ With the amount of anxiety and fear in the room, John’s confused. Then again, Beckett _did_ decide to come to Atlantis. He must be a tough Omega. 

“Anything you want to talk about?” John asks, even as he silently pleads for Beckett not to say anything. He’s probably going to end up not only hugging Beckett, but having to ‘talk’ as well. Say soothing things. He wonders if he can call Lorne down here as a pre-emptive measure. Lorne’s good with Omegas. He manages to cuddle them and then send them on their way - full of oxytocin and happy feelings. John always just ends up feeling stuck and trapped. “Or maybe you want me to have a chat with McKay - Alpha to Alpha.”

Beckett opens his mouth and then closes it. “No. Thank you, Major.” John can’t help but feel relief as Beckett seems to give himself a little shake. “Now. What can I do for you?”

***

John can admit, he was a slightly nervous to have two Alphas - him and McKay - on a gate team. Sometimes in high-pressured situations, Alphas start butting heads and end up causing more trouble than it’s worth. John’s seen it happen in the military which is why they tend to limit the amount of Alpha interaction during intense times. But for all that McKay can be abrasive and sharp, he doesn’t seem to have a problem following orders in the field. He sticks to the science and leaves the military decisions to John. It turns out, they get along pretty well when they’re not gating as well - having meals in the mess and screwing around with Ancient tech. John will never get the look on Elizabeth’s face out of his head when he pushed McKay over that railing. 

He also won’t forget the look on McKay’s face as he walked into that energy cloud. John doesn’t want to lose anymore expedition members, but losing McKay would be a horrific blow. There’s a reason he was picked as the head of the science team and John’s not sure how they would get on without him. He shudders to think of the other Alpha scientists they’ve got - Kavanaugh and Heightmeyer. Kavanaugh is one of those posturing Alphas. He and McKay get into it pretty often - their shouting matches are legendary, driving some of the Omega scientists out of the labs, unable to handle the stress. Kavanaugh doesn’t know when to quit. He may be an Alpha, but so is McKay and McKay’s his boss. If Kavanaugh were in charge… John’s willing to bet the entire science department mutinies in three days. 

As an Alpha, Heightmeyer would be great for the emotional stability of the scientists, but she’s a soft scientist and John’s not sure she’d be able to keep up with the hard physics, biology and chemistry of the Atlantis team. 

John figures McKay’s what they call a ‘Cold Alpha’ - generally not noticing when Omegas are stressed out, pumping anxiety and nervousness into the air. If Cold Alphas do notice Omega stress, they don’t tend to do anything about it. John’s seen the Betas react before McKay does, doing their best to help out their more sensitive colleagues - dolling out hugs or kind words. McKay just… keeps working and expects his scientists to do the same. Something about watching him work _does_ seem to keep the Omegas from having breakdowns. Although Zelenka may be coming close. He’s the highest ranking Omega in the sciences, second in command under McKay - another thing that Kavanaugh has a beef about. Kavanaugh has made his opinion on Omegas more than clear - they shouldn’t be in the sciences, they shouldn't be in high pressured jobs and they sure as hell shouldn't be on Atlantis. John’s got a feeling Kavanaugh’s one of those Alphas that thinks Omegas should be at home, having babies and taking care of families. There’s a few Omegas on Atlantis who would sock his teeth out if he dares says it. Beckett being one of them. 

Luckily, McKay seems to have no such allusions about Omegas. He and Zelenka work well together. John read in the personnelfiles that McKay’s the one that recommended Zelenka for the position. It’s not unheard of for Omegas to have high level positions, but it’s rare. Zelenka’s good, but he _is_ an Omega and just not biologically built to handle the level of stress Atlantis puts on them. Omegas don’t have the same adrenal responses - their system sends them into heightened states of panic more easily, releasing copious quantities of fear inducing hormones. They also don’t come down as readily from pressured situations. Studies have proven they have more pain receptors and simply ‘feel’ things both physically and mentally more than their Beta and Alpha comrades. In John’s opinion, Zelenka needs a more touchy Alpha, but he’s not going to get that from McKay. 

Which John can understand. Hell, he doesn’t like being a touchy Alpha either. At least he’s in the military and there are precious few Omegas there. Mostly Betas with Alphas sprinkled about, like Lorne and Bates. However, if something _were_ to happen to McKay (and it makes his gut twist uncomfortably to think of it), John’s preference would be to put Zelenka in charge. He doesn’t know how the rest of the expedition would feel about that, or if Zelenka could handle it (provided he even accepted). They’d probably have to send Kavanaugh on an extended (read: permanent) gate trip. John’s a firm believer that your biological dynamic doesn’t have to rule you, but he also knows that sometimes they only have seconds to make a decision. With the way their biology is built, Omegas have a harder time making those fast decisions.

Well, as long as nothing happens to McKay, John won’t have to worry about it. 

***

Sleeping in a hospital or medlab is always more like resting with your eyes closed than actual sleeping. John can never quite relax with the noise around him, eyes slitting open as nurses go to and fro, doctors bustle about, orderlies do their job. He’s not sure if it’s an Alpha thing, a military thing or just a ‘him’ thing, but he figures he only has to make it one night and then Beckett will release him. After being stuck with that Wraith-like parasite on his neck, John’s more than happy to stay the night in the relatively well-lit medlab with no one the wiser about his current reluctance to go back to his small quarters. Where he have to try to sleep in the dark. Where things would start to feel like they were crawling on him. Or making a chittering sound. 

He can still feel the strange, sucking-pulling sensation all around the wound on his chest. He didn’t mention it to Beckett, but the doctor’s Omega senses must have been ‘tingling’ because he mentioned that John might have some residual feelings from the parasite as the tissue heals up. He’d offered John a numbing spray and dammit, John should have said yes. Damn Alpha pride. 

He hears the doors of the medlab swoosh open and then McKay’s sharp tone. John opens his eyes just a skoosh - just enough to watch McKay look around the medlab, searching for something. His blue eyes linger on John for a moment and John fights the urge to fidget or move. He can barely make out McKay where he stands - just inside the doorway, watching John from where he’s stopped. The look on McKay’s face - careful, curious and contemplative - makes John want to… do something. He’s not exactly sure what. 

Or if he is, he’s not sure he’s ready to admit it. 

Beckett comes around the corner, presumably from doing nighttime rounds and stops short at the sight of McKay. 

“It’s three in the morning, Rodney, what are you doing here?”

“I’m out. Or I will be tomorrow.”

“At three in the morning you decide to deal with this,” Beckett replies dryly. John has to strain to hear them - the sounds of medlab threatening to obscure their conversation. “I’ve told you to watch your dosage more carefully.”

“You know I don’t always need it. I can’t tell when I’m going to run out.”

“You could bloody well make sure it wasn’t at three in the morning.”

McKay waves his hand. “I was up working. And so are you.”

“Aye and that’s another thing I want to discuss with you. You can’t keep this pace up.”

“I know my limits.” McKay’s reply is accompanied by the mulish jut of his chin that John’s come to recognize well. 

“Well, I know biology and I’m telling you, extended use of the cocktail coupled with the stress of Atlantis is going to take its toll. Biologically - ” 

“Biology,” McKay interrupts. “I’m still not sure it’s a real science.”

“It’s real enough to help you keep up this farce. What are you trying to prove?” Beckett pauses, mouth firm and then says, “I think you should go off the cocktail.”

“Are you insane?” McKay’s voice comes out like a firecracker and he looks around, directly at John’s bed as if checking John’s still asleep. John’s barely got one eye open - able to see, but he’s sure from the distance it will look like he’s asleep. He and his brother used to do this all the time as kids - fooling their mother and father both. 

“I can’t go off it,” McKay continues. “Do you know how much depends on me being in charge of the science team? Do you know what will happen if I’m found unfit for duty? Kavanaugh, Carson. That’s what will happen. How well do you think the team will do with that? Never mind all of my research will be called into question, any discoveries I’ve made will have to be re-vetted-”

“Rodney,” Beckett says, cutting him off and reaching out to put a hand on McKay’s arm. “Keeping this up, in another galaxy, was a long shot at best. You must have known that.”

McKay pulls his arm back sharply from Beckett. John would think a rebuff like that from an Alpha would have the Omega in Beckett cringing back - Omegas are notoriously sensitive to any kind of physical rejection. Instead, Beckett just looks… perturbed. 

“It was a short term solution at best, Rodney. You’ve been doing this far too long. The damage you’ve already done-” Beckett’s voice breaks off and he looks at McKay so… forlornly. For a moment, McKay looks just as sad, but then he squares his shoulders.”

“Marie Curie…”

“Died, Rodney. She died. Of exposure.”

“But look at the legacy,” Rodney continued. 

“Spare me the Marie Curie speech again. I know my history.”

McKay stares at Beckett and Beckett matches his stare. Wow. Beckett’s a good doctor. Most Omegas can’t hold an Alpha stare, but Beckett’s not backing off. 

“Sheppard will take me off the gate team.”

John’s brain runs over what he’s hearing. Take McKay off the gate team? Marie Curie dying? Just what the hell is McKay on and what does it do?

“You don’t know that. Major Sheppard seems to be very reasonable and progressive.”

McKay makes a scoffing sound, waving his hand dismissively. “Yes, yes, yes, he’s a god among Alphas, all hail the Major.” McKay’s words are harsh, but something about his tone is…. Fond.  
“Sheppard can pretend to be ‘reasonable’ when he doesn’t actually have to make the decision, but as soon as it’s out there - ” McKay snaps his fingers. “I’m off the team and goodbye Nobel.”

The way Beckett and McKay argue is like an old married couple, John thinks again. It’s odd they aren’t together - Beckett’s clearly not afraid to stand up to McKay and while McKay doesn’t agree with him, he’s not throwing his Alpha weight around and ordering Beckett to do anything. 

“Rodney… This isn’t good for you.”

“I told you, I know my limits. Besides, we’re bound to find a ZPM on one of these planets and as soon as we do, I can cut my hours back.”

Beckett’s shoulders slump. Whatever they’re arguing about, McKay’s won. “I’m going to hold you to that,” Beckett says. “Come into my office. I’ll do a blood draw to check your numbers and get you a refill. But you have to remember, if we don’t regain contact with Earth or find a substitute here, you’re on a clock anyway. I don’t have an unlimited supply.”

“ZPM,” McKay sing-songs, following Beckett into his office, obscuring them both from John’s eyes and ears. 

What the hell?

***

McKay takes orders extremely well in a hostile situation, but also knows when to follow his own gut, a thing for which John is incredibly grateful. When he left Gall and McKay behind on the Wraith ship, he’d thought it was for the best. With an injured Beta and two Alphas, he did the math. McKay would have to stay with Gall and John would go after the Wraith to stop him, it, whatever before it got to the ‘jumper. 

But then McKay shows up, just when John needs him, firing on a Wraith. He’s inexperienced in a battle situation - most civilians are - but he keeps commendably calm, going so far as to simply ask John what to do next when his gun is empty. John tells him to reload and McKay does it efficiently. He’s never been so glad to have two Alphas on a mission in his life. 

He’s not sure what would have happened otherwise. With the scientists dead (he assumed at the time and later confirmed it with McKay), and John slightly wounded, he doesn’t know what he would have done if he’d had to take care of someone. 

McKay may not be a typical Alpha, but John’s more than happy to have him on the team. 

***

It’s not like things were going great in Pegasus, but still, John’s surprised when their latest mission goes completely to shit. 

They just got finished with that Wraith and losing two scientists. McKay’s taking it hard. As an Alpha, John feels for him. It’s tough to lose team members. The Alpha in John feels every loss in Pegasus as a personal failure - a black mark on his Alpha-ness. Heightmeyer’s been trying to pin him down and get him to go to a session about it, but so far John’s be able to dodge her. 

If something else goes pear shaped, she’ll be merciless. She’ll want him to talk. About feelings. And… stuff. 

This can’t be the mission that goes pear-shaped. Not like this. 

The Bika are dynamic- Alphas, Betas and Omegas. John has no issues with the Athosians, but he thought it would be kind of nice to be around people with the same social structure as the expedition. 

He takes that thought back now. 

He’s been a hostage now for twenty earth hours. He figures he’s got at least another hour before he might expect some kind of action from Atlantis. Although, knowing Weir, she’ll try every negotiation trick in the book before she’ll authorize Lorne and Bates to plan out a rescue. John can only hope Weir doesn’t review the fact that McKay and Sheppard are the two highest profile Alphas on Atlantis and they’re on the same gate team, which means when one gets taken hostage, they’re both taken hostage. 

It’s some kind of internal coup, two Alphas jockeying for power and god, the more things change (different planet, different galaxy for crying out loud) the more they stay the same. John, McKay and about 50 Bika are in a large theatre being ‘guarded’ by a group of what appears to be rebels. Heavily armed rebels. At least, John thinks they’re rebels. It’s so hard to tell when you jump into the middle of a plot. Teyla and Ford were on an agricultural tour and John is running under the assumption they made it back to Atlantis. Ford’s young and inexperienced, but Teyla is not and John has faith she got them out and is already rousing the cavalry. 

McKay shifts next to him, his body a tight coil. John knows how he must feel. It’s the damn pheromones. Ballpark, there’s about fifteen Omegas in the room, all stressed out and anxious, their bodies flooding with epinephrine, adrenaline and a host of other hormones. It makes the air thick and heavy with nerves and fear. In the twelve hours they’ve been in the theatre, John can see several Alphas trying to step up and help the Omegas but there’s just not enough Bika Alphas to go around. John can see across the room where there’s an Alpha who’s corralled three Omegas close to herself and is trying to keep them calm, sitting tall and straight with one practically in her lap and the other two pressed close to her side. For whatever reason, the Bika are Omega-heavy - more Omegas than Alphas. It’s not unheard of in some small groups on Earth especially when procreation is an issue - if you need to ensure survival, you need more child-bearers. The dynamic genes are complicated - not just a simple Alpha/Beta/Omega switch, but researchers do know, the genes respond to sociological pressures and survivalism. Maybe it’s just the way the Bika are, but it’s tough in stressful situations. For everyone. 

He and McKay might have to step in and help out. It’s hard to know how their Omegas will respond. John and McKay are foreign Alphas - unknown, strange, travelers through the gate. John didn’t get enough of a sense of the Bika to know if that’s going to be a problem or not. They might just make it worse - Alphas muscling in on fearful Omegas and sending them deeper into panic. The last thing they need is for any Omegas to go into a full-blown Omega Breakdown. John’s nose twitches. Although, they might not be that far away from that happening. The cloying, syrupy scent of ‘Omega in distress’ is overwhelming John’s nose and he’s not even that close to any of them. He can’t imagine what it must be like sitting right next to them. 

McKay shifts again, fingers twitching. Probably itching for his tablet. There are energy signals on the planet and McKay would probably rather be using his time in captivity so to speak doing actual research. McKay’s leg starts jigging - like a nervous tic. John’s eye is drawn to the movement. McKay’s usually always moving - hands gesturing, fingers snapping, eyes darting around and taking everything in. But this is different. This is like… fidgeting. Maybe the pheromones are getting to him. John leans a little closer to him, tipping his head down so he can speak closer to McKay’s ear. The last thing he wants to do is draw any attention to them. As he does, he breathes in, preparing to speak. 

He’s nearly overwhelmed by the smell of Omega. He swallows hard, feels his brow furrowing. He leans in a little closer. McKay’s head sharply turns to John, eyes bright blue and clear, but not sharp like John’s used to. Not assessing. 

Wide. Frightful. Panicking. 

John looks over McKay’s quickly. Sweat on his upper lip, skin chalky and pale, flared nostrils, hunched in on himself, fidgeting. 

“What?” It comes out like a hiss from McKay’s lips, mouth tight and slightly turned down at the corner. 

John breathes in again, knowing what he’s going to say, but not quite believing it yet. A kaleidoscope of images rotate and shift through his mind. McKay’s inattentive to the Omegas in the science contingent, not ever really noticing when they need soothing or comfort. McKay’s ability to take military orders in tense situations - he’ll fight if he’s got the science to back it up, but otherwise, has never given John the normal problems he’d expect from having another Alpha on the team. The way Beckett and McKay interact - not at all like an Alpha and an Omega, John realizes, but an Omega and a friend, a peer - another Omega.

“You’re an Omega.”

McKay opens his mouth, closes it and then looks around, checking his surroundings. Jesus, not only is McKay an Omega, he’s an omega that's been in a hostage situation for over twelve hours. 

“How?” John starts, not sure what he’s going to ask. How has McKay been pulling this off? How long has he been masquerading as an Alpha. He sees McKay’s hands ball tightly into fists, the muscles of his jaw flexing as he clenches his teeth. McKay’s eyes dart around again, checking his surroundings. Trying to make himself feel safe. 

“Jesus, come here,” John says, his inner Alpha doing a better job of running things at the moment than his brain. He wraps an arm around McKay and tries to tug him closer, feeling something that has been strung tight inside him since he came to Pegasus finally relax and settle. 

McKay goes stiff and hard under John’s arm. “Don’t,” he says, pulling away, his entire body uncompromising and unforgiving under John’s hand.

“I’m sure you know this, but you’re on the verge of a full-fledged Omega Breakdown.”

“I don’t need you to tell me that, Major,” McKay says, voice thin and low. He tries to shuffle his butt on the ground to move further away from John. John tightens his grip, keeping McKay from moving. An Alpha sitting about ten feet away gives him a strange look, probably wondering what the hell is going on. In his eyes, McKay’s an Alpha and John’s trying to… well… cuddle him for lack of a better word. 

“You need to let me help you,” John says. 

“I don’t need anything,” argues McKay. “It’s just stupid biology.”

“Well, stupid biology is making you hyperventilate,” John says dryly, hearing the quick wheezing starting to come from McKay’s lungs. He tries to pull McKay closer again and he thinks that McKay’s just about to give in when there’s a sudden loud noise - a blast of light - and then Teyla, Lorne, Ford, Bates and a contingent of marines are pouring in the door. McKay shuffles away from him quickly, back ramrod straight. 

Rescue has never been so wanted and so… annoying. 

***

John never realized how much _stuff_ there was to do after a gate mission gone wrong until he wanted to talk to McKay separately and isn’t able to because of paperwork, debrief and medical examinations. 

He can see McKay getting examined by Beckett, see how their heads are tipped together, see the way they both turn to look at him and then away again quickly. John wants to go over there, to talk to McKay to _do_ something but he can’t because Lorne and Weir need to know exactly what happened with the Bika and if they can still be considered friendly or if they’ve moved into the ‘hostile’ territory. 

Twelve hours later he’s done reporting and debriefing and submitting to exams and questions and queries and he’s _finally_ able to make his way to McKay’s quarters. He feels like a college frat boy - sneaking over to the girls’ sorority house - furtive glances in case he’s caught, nervous like he thinks someone will challenge his reason for seeing McKay at 3 in the morning. Which, if they knew McKay was an Omega, they _would_. There’d be knowing looks and maybe some snickers. But, as an _Alpha_ , McKay has no such limitations put on him. 

He leans on the door chime, finding it extraordinarily loud to his ears, and waits, his ears straining to hear anything from behind the door. When McKay does answer, his lips are in that side-slant that John recognizes well. It means McKay’s unhappy, displeased and about to launch a rant about something. 

“May I come in?” John asks. A flicker of surprise crosses McKay’s face and it takes a moment for John to realize why. Alphas don’t ask Omegas for permission. Alphas _take_. Alphas enter when they wish and do what they want when Omegas are involved. McKay’s surprise is because he didn’t expect that from John. 

It makes John very careful as McKay steps aside and indicates John may enter. 

John’s never been in McKay’s quarters before. They’re in disarray - computer components, ancient tech, clothes and workout gear lying around haphazardly. John catalogues and compartmentalizes what he sees. The computers for McKay’s work, the ancient bits also for McKay’s work, the workout gear… oh. McKay wouldn’t have the natural testosterone to be bulky and strong like an Alpha. He’d have to work at it. Ever since John realized McKay was an Alpha, he’s been thinking about how much effort it would take to keep up the extraordinary charade that McKay has concocted. Medical records, social interaction, physical appearance, test scores… there’s so much to McKay’s deception, John’s mind boggles. 

“I was expecting you,” McKay says, voice terse. “So. What’s it going to take?”

“Pardon?” John asks, confused.

“For you silence, what’s it going to take?” McKay’s chin juts out and he matches his gaze to John’s. John looks away. 

“I’m not here to… blackmail you, if that’s what you think.”

McKay huffs, crossing his arms over his chest. “Really? You just happened to pop by at three in the morning to discuss the fact that I’m an Omega.”

John’s eyes snap back to McKay. Everything falls into place now. Of _course_ McKay is an Omega. McKay’s seeming blindness to Omegas in his charge being in distress, his ability to take orders in the field without question, his reputation as a ‘cold Alpha’ - not reaching out and engaging in physical contact with Omegas, the slight twisting, _wrong_ feeling in John’s gut whenever he’s watched McKay go toe-to-toe with a foe, a colleague, a coworker. On some level, John thinks maybe his body knew McKay wasn’t an Alpha. Or maybe hindsight is twenty-twenty. 

When John thinks about their missions… Jesus, John has been traveling off-world with an Omega this whole time. He’s left McKay alone, he’s handed him a gun and let him defend himself, he’s seen him argue with Kavanaugh, debate with Elizabeth, fight with Bates. Christ, McKay faced down a Wraith, a _Wraith_ and without him, John would probably be dead. 

“How long?”

“That’s your first question, how long?” McKay snorts. “I suppose there’s no harm in telling you now. I’ve been an ‘Alpha’,” he makes air-quotes around the word, “since I was nine.”

John can feel his eye bug out. “Nine?” he repeats. 

“Nine,” McKay replies, his chin coming out further. “Let’s get this going, Major. I’ve got several simulations running in the lab that I need to check on soon. Usually blackmail takes the form of money, but since we’re stranded in Pegasus, that’s hardly going to work. Also, you’re rich; I’ve read your files. I can only assume you want something else for your silence.” McKay’s lips twist in an ugly manner, his eyes moving off to the side. It takes John a moment to realize what McKay is implying by the dejected slope of his shoulders and the cruel twist of his lips. 

“What? No, Jesus no. I came here… I just…”

“Let’s just get it over with, Major,” McKay says, moving his arms to take off his shirt. His movement finally makes John dart forward, halting McKay’s arms where they are. McKay looks… confused by John’s actions. And afraid. John moves closer, waiting for McKay to bolt. He inhales deeply and… doesn’t smell anything ‘Omega.’ Instead, he gets a strong scent of ‘Alpha’ permeating his nostrils. 

John doesn’t move his hands from where they are around McKay’s wrists, keeping McKay from moving. “Beckett’s got you on some kind of blockers. Keeps your Omega pheromones under control and makes you release Alpha scents,” John reasons.

McKay’s jaw works silently. “And they work pretty goddamn well until I’m on some god-forsaken planet being held hostage and miss a dose.”

 _That’s_ what happened on Bika. Rodney was off his cocktail. The same one he and Beckett argued about the other day. John feels McKay’s arms go a little more relaxed under John’s hands. 

John doesn’t know what to say. Apparently, neither does McKay. He stands stock still, not yanking his arms from John’s hands, not moving backward. John’s higher brain is confused by the knowledge that McKay is an Omega, but it feels like his lower brain, his animal brain, is finally satisfied to have McKay before him. He leans forward, giving McKay plenty of time to move away, to push at John, yell at John. 

But McKay doesn't. 

He stands stock still as John wraps his arms around McKay and then pulls him close, into John’s body heat, into his personal space. As on Bika, McKay is stiff, unyielding under John’s touch. It’s like holding a marble statue. 

“What are you doing?” McKay asks. 

“I’m trying to help,” John replies. Unlike when he’s been ‘stuck’ comforting Omegas in the past, this doesn’t feel like a trap to John - like something that has to be done, like a chore that requires attending. He wants to do this. 

“I don’t need help,” McKay says, body still tense and hard. 

John doesn’t relent. He tightens his grip, pulling McKay even closer. He wonders how long it’s been since McKay has even felt the touch of an Alpha. If he’s been pretending to be an Alpha since he was nine…John doesn’t imagine there’ve been many opportunities for this. 

There’s a moment when McKay inhales and his body tenses like he’s gathering his strength to pull away and then… he relaxes. Infinitesimally. A minuscule movement of his shoulders, but John feels it. Then, McKay’s arms shift, then his hips, then his knees and McKay is no longer a marble statue pressed against John, but instead is a soft weight. McKay inhales again, turning his face slightly to John’s neck, where John knows his Alpha pheromones are pumping out large quantities of calming scents - his biology more than ready to comfort the Omega near him. Like a large predator in the wild, John’s afraid to move - afraid if he shifts so much as a millimeter, he’ll spook McKay and never see him again. He keeps his body as still as possible and then feels McKay’s shoulders sag, releasing some of the tension that’s constantly in them. McKay doesn’t raise his arms, doesn’t burrow into him like Omegas sometimes do with Alphas, but he does seem to relax infinitesimally.

“I won’t tell anyone,” John says, making his voice as soft and calm as he can. 

McKay - Rodney - inhales again, his breath hitching slightly. “Okay.”

***

John goes to Rodney’s quarters the next night. And the next. And the next. He waits until it’s late enough that the hallways are mostly empty, not that anyone is keeping attendance records of where people go and what they do, but John smart enough to know that someone like Rodney who’s spent years hiding his true nature would prefer a little discretion. 

While he and Rodney interact during the day - exchange their same banter, argue about what to do with an entry in the ancient database (plan away mission, do not plan away mission), trade ideas on what the latest found gadget does - at night it’s different. At night, John sits on the small couch in Rodney’s quarters and… waits. Rodney will always sit too far away and John waits. Rodney won’t say anything at first and John waits. Rodney will start to talk about the day, explaining things in the science lab and John waits. Rodney will be drinking too much caffeine and have too many computers open and John waits. 

Finally, Rodney’s shoulders will drop , his body will relax and then John will know it’s okay to move closer to him, to settle an arm around Rodney and let him breathe into John’s neck. 

He comes to Rodney’s quarters one night and instead of going to the sofa to have a seat, Rodney stands there, in front of John, arms crossed over his chest, face defiant. 

“Why do you keep coming here?” Rodney asks. 

“Good to see you too, McKay,” John drawls. It amuses him that Rodney finds it annoying. 

“I’m a horrible Omega. Look at this place. It’s a mess” Rodney gestures wide and John checks out the room. Computers, ancient tech, socks, a tray from the mess - Rodney clearly doesn’t pick up after himself. 

John looks around at the space again, eyes narrowing. “I think your quarters are bigger than mine.”

Rodney rolls his eyes. “I also don’t have time to cook.”

“No one’s asking you too.”

“I won’t fawn all over Alphas. Never have. Don’t see the point.”

“Okay.” John shrugs. 

“It’s not that I can’t do those things. I’m quite proficient. My soufflee makes grown men weep and you’ll never taste a chicken cordon-bleu as good as mine,” Rodney says, one of his palms coming to rest over his heart. “It’s that I _don’t_.”

“All right.”

Rodney is undeterred. “I’m going to win a Nobel prize. I work long hours.”

John huffs. “I know how long your hours are, McKay. I’m working the same ones.” 

“Even when we re-establish contact with Earth, even if someday I go back to live on Earth, I’ll still work these hours.”

“Fine.”

“I’m horrible to live with. I’m up all the time working and the cocktail gives me insomnia.”

“It’s not like I’m living a life of leisure here,” John says easily. 

“If you’re looking for an Omega to pander to you or take care of you after a busy day, I won’t do it.”

John rests his hands on his hips and shrugs again. “I take pretty good care of myself.”

Rodney seems unsure what to say next. He purses his lips together and then squares his shoulders. “The cocktail I’m on has completely fucked my system. I’ll never be able to have children.”

John’s only just barely manages to keep his eyes from bugging out at the mention of kids. Jesus. Their in the middle of a war-zone out here. Plus, kids have never been on John’s radar. Other people’s kids are okay. From a distance. “Understandable,” he says. He can only imagine what the hormone suppression has done to Rodney’s body, but he figured it couldn’t be without side effects. 

“Nor would I want them anyway,” Rodney continues. “I’m sure that goes against every Omega stereotype you’ve heard, but I don’t find them hopelessly endearing or undeniably cute. They’re messy and annoying and take up too much time.”

“Fair enough.” Johns steps over to Rodney’s sofa and sits down, shifting a bit to get comfortable. 

Rodney looks completely annoyed and frustrated. “Then why are you still coming here?” he asks again, his tone plaintive. 

John props his feet up on the coffee table. “Maybe I like the company.”

***

John thought he did a fair job making it understood that he didn’t expect Rodney to be some kind of Alpha wet-dream Omega. Truth be told, watching Rodney explain his idea with the lightening rods and powering the shield, coupled with Rodney basically ordering him to two grounding stations was sort of hot. John knows Rodney thinks his inability to be a textbook Omega is a drawback, but if anything, it’s a turn-on to John. Rodney is capable. Rodney is smart. Rodney could run circles around half the Alpha’s John knows and then some. 

That doesn’t mean, however, that John isn’t about to go bat-shit insane and kill everything in his path when Rodney and Elizabeth are held hostage by the Genii. John wants to tell Kolya if he so much as _looks_ at McKay in a way that’s threatening, John will use Kolya’s innards for piano string. 

But he can’t. 

Because Kolya thinks he’s got two Alphas hostage - Weir and McKay. If he knew that Rodney was an Omega… if he thought for a moment he could use that against John or Rodney…. Omegas are thought of as soft. Malleable. To be protected. Kolya would simply threaten McKay and goddamnit, John would probably do whatever Kolya wanted. 

John’s got to be smart about this. He’s got to think like Rodney. Up until now, he’s marveled at how Rodney’s been able to pull of his charade - the lengths he’s had to go to - social interaction, physical posturing, forged medical records. But it’s suddenly more _real_ to John than it’s ever been before. Rodney’s _life_ depends on his ability to play an Alpha convincingly. Kolya may threaten and try to intimidate another Alpha, but he’d rip an Omega to shreds to get John to comply. The Genii are scarily similar to Earth in their A/B/O dynamics and John knows if Kolya finds out McKay is an Omega…. 

He takes a breath and checks his ammo. Secure McKay. Secure Atlantis. Those are John’s priorities. 

His gut twists when Kolya tells him he knows about Rodney’s plan for Atlantis with the lightening rods. It’s not like Rodney would just _share_ that info. What happened up there? Why did McKay talk? John feels about thirty seconds away from becoming one of those feral Alphas he hears about on the six o’clock news - going hay-wire because their Omega was in danger, or hurt, or trapped. John always wondered if maybe those Alphas were already unbalanced before they went crazy because he’d never once felt like he was about to lose all his control and start beating the shit out of people, breaking anything that gets in his way, doing things to the people that scared his Omega just to feel them _hurt_. 

John kills two Genii at one of the grounding stations and though he’s never taken _any_ joy in killing, part of him feels deeply satisfied at their deaths and he wastes no time letting Kolya know. He regrets it when Kolya retaliates and pronounces he’ll kill Weir. Although, while losing Weir will be a blow, John can’t help the rush of relief that it’s Weir Kolya threatened and not Rodney. 

When he activates the gate shield and hears a dull thud for each dead Genii trying to materialize but unable to make it through the event horizon… he shouldn't feel better, but he does. 

John doesn’t get the chance to kill Kolya and the loss leaves something sour and metallic in his mouth. He wanted to make Kolya bleed, wanted to wound him, wanted to gnash his teeth together and see fear in Kolya’s eyes. Instead, he sees Kolya fall through the gate after John shot him, but John knows it wasn’t a kill shot. He couldn't get one with Kolya using Weir as a shield. 

The even horizon dissipates and John has a moment where he wants to demand they fire up the gate so he can go after him, but…. Atlantis. Rodney. 

Rodney is already moving toward the controls of Atlantis, intent on saving the city, working to activate the shield. With the Kolya gone and the Genii taken care of, John wants to bat Rodney’s hands away from the console and take him somewhere quiet, somewhere _safe_. 

But, he can’t. 

He takes two steps toward Rodney and and realizes he can’t. He can’t do anything. Because McKay is supposed to be an Alpha. And Alphas don’t comfort other Alphas. Alphas don’t run their hands over other Alphas and check them for injuries. Alphas don’t wrap their arms around other Alphas and let them breath into the soft spot in their neck, letting them soak up calming pheromones while at the same time take comfort in the security and well-being of other Alphas. 

John has to wait while the storm rages, while Teyla, Sora and Beckett finally arrive, while Rodney activates the shield. The side of Rodney’s face is swollen and John bets that if he had to make a match, the size and shape would match Kolya’s fist. Then he sees blood on the sleeve Rodney’s arm, a gape in the fabric where it’s torn, a glimpse of flesh showing through and he knows now why Rodney told Kolya the plan for Atlantis. 

John’s going to kill Kolya the next time he sees him. 

Rodney plays off his injury, joking that he had to bandage it himself because Beckett wasn't’ able to, but it’s ludicrous. There are other nurses and doctors in medlab, but Beckett’s the only one that knows Rodney’s an Omega. John’s willing to bet that Rodney _can’t_ go see anyone else, lest it leads to a sample or tests and having his secret exposed. 

John’s eyes track Rodney as he moves around Atlantis, unable to go back to his quarters until they’re sure the storm has passed and he’s tested all the systems to ensure they didn’t overload any equipment or permanently damage any systems. 

It’s late, so late, much to late, by the time John arrives at Rodney’s quarters. He rings and while Rodney doesn’t answer, the doors slide open, letting him inside. 

“Rodney?” John asks. His quarters are dark. Rodney’s never _not_ met him at the door - usually with a slightly perplexed frown on his face. John takes a few slow steps around and then hears something from the bathroom. The light’s on, a sliver of white coming from under the door. He can hear the water running. 

“Rodney,” John says again, pressing a hand to the door. The water shuts off and there’s a pause - a moment of no sound, no movement from behind the closed door. John wonders if he should open the door, break it down if it’s locked, but then it slides open and Rodney stands before John, face ghostly pale. He’s shivering finely - minute tremors that are almost imperceptible to the human eye. Almost. 

“I can’t… it’s still bleeding and Beckett’s… and I can’t make it stop,” Rodney babbles, holding his arm out. The bandage that was overtop of his uniform is gone and the sleeve is rolled up. John can see four long gashes cut into the tender skin of Rodney’s inner arm. “It needs stitches and I can’t with my hands shaking.”

Looking past Rodney into the bathroom, John can see a first aid kit and what looks like the start of a suturing station. He reaches up and pulls Rodney in close and for the first time, Rodney goes completely pliant and relaxed instantly, automatically turning his face into John’s neck. John cups the back of his head, feeling the soft, ultra-fine hairs there, kneading the area slightly with his fingertips. Rodney’s breath hitches in and a soft of broken sound escapes from him and then he’s silent again, body still shaking. 

“I can fix it. It’s all right. You’re all right now,” John says. 

A large shiver runs through Rodney’s shoulders and he presses his nose into the soft hollow of John’s throat. The tip of it is cold against John’s skin. 

“You’re all right,” John repeats. He’s not sure if he’s reminding himself or Rodney. 

***  
Fin

 

 

 

**Bonus material - I wanted to fit this in the story, but… couldn’t make it work. But if you’re interested, here’s some of Rodney’s back story….**

“Why did you start pretending to be an Alpha when you were nine?” John asks. 

“It wasn’t like I thought it out all the way or anything. Not then,” Rodney says, leaning into John’s side, starting to relax. Rodney sighs and then continues, “My mother was an Unstable Omega.” 

John knows the type. While Omegas are softer, often more timid people, sometimes they can be volatile. Unstable Omegas are overly needy, anxious, unbalanced. They can have the best, most dedicated Alpha in the world and it won’t settle their biology. 

“What about your father?”

“He was a Cold Alpha. All I remember growing up is fighting or crying or both. He left when I was eight.”

“And that left you alone with your mother.”

“I have a sister. Jeannie. She’s a real Alpha, but she was only three when my father left. Someone had to be in charge and my mother was incapable. After my father left, she was a mess. She couldn't take care of herself, let alone us. She would go days without leaving her bed - there’d be no food in the house, no laundry done, no structure or order. About a month after my dad left she showed up at my school and called me out of class because she said someone had to come and take care of her.”

“She meant you?” John asked, unable to keep the incredulous tone out of his voice. 

“She meant me,” Rodney repeated. “So I did. I figured the bank accounts, figured out that though my father had left, he wasn’t a total asshole and was depositing money for us. I learned what children were supposed to eat, when to register Jeannie for school, how to go shopping, how to pay bills.” Rodney shifted on the couch, resting further into John’s space. John moved his hand up and down Rodney’s spine. “I started noticing people treated me like an Alpha. Obviously I was a child, but the way I was running the household, people assumed I was precocious Alpha, stepping in to help his Omega mother. I was too young to put out many pheromones and no one really got that close to me anyway. I pulled myself out of my current school, changed my records and enrolled myself in a different one, this time as an Alpha. And no one knew the difference. I learned enough chemistry and biology to make some fake pheromones and worked on my habits and behavior. I was careful not to get sick or hurt - a hospital test would be impossible to fake. Until I met Carson when we were twenty and more or less bullied him into helping me.”


End file.
